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Author Topic: Color each block nucleotide at each locations  (Read 2495 times)

Offline spark159

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Color each block nucleotide at each locations
« on: May 26, 2021, 03:43:15 pm »
I know I can color according to nucleotide type (like A, T, C, G).
But is it possible to color each block nucleotide at different location with different user-defined color?

For example,
nucleotide at residue 1 -> yellow
nucleotide at residue 2 -> purple, etc

Offline xiangjun

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Re: Color each block nucleotide at each locations
« Reply #1 on: May 26, 2021, 04:18:58 pm »
No, at least not automatically. That said, you could manually select each nucleotide and then color it whatever way you want.

Offline spark159

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Re: Color each block nucleotide at each locations
« Reply #2 on: May 26, 2021, 04:19:42 pm »
Thanks for reply!

Could I know how to do in pymol-plugin ?

Offline spark159

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Re: Color each block nucleotide at each locations
« Reply #3 on: May 26, 2021, 04:23:47 pm »
I tried it in pymol, but only the color of real nucleotide was changed, not the color of "block".

Offline xiangjun

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Re: Color each block nucleotide at each locations
« Reply #4 on: May 26, 2021, 06:06:18 pm »
Please provide reproducible examples, illustrated with screenshots if necessary. Otherwise, I (maybe many other viewers of the thread) cannot understand exactly what you are talking about.

Offline spark159

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Re: Color each block nucleotide at each locations
« Reply #5 on: May 27, 2021, 02:40:11 pm »
Thank you so much for reply!

Here is example,

I made block image of pdb file:
x3dna-dssr -i=6rjg.pdb --blocview=png-c3 --block-file=wc-minor -o=6rjg.pml

I loaded pml file and I selected one nucleotide in pymol as figure I attached.
And type "color red, sele" to change the block color from blue to red.

But the block color (which I selected) is not changed, but I think the color of nucleotide embedded in the block is changed instead.
Do you have any suggestion to change the color of particular block of nucleotide which I selected?

Thanks

Offline spark159

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Re: Color each block nucleotide at each locations
« Reply #6 on: May 27, 2021, 02:41:46 pm »
Thank you so much for reply!

Here is example,

I made block image of pdb file:
x3dna-dssr -i=6rjg.pdb --blocview=png-c3 --block-file=wc-minor -o=6rjg.pml

I loaded pml file and I selected one nucleotide in pymol as figure I attached.
And type "color red, sele" to change the block color from blue to red.

But the block color (which I selected) is not changed, but I think the color of nucleotide embedded in the block is changed instead.
Do you have any suggestion to change the color of particular block of nucleotide which I selected?

Thanks

Offline xiangjun

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Re: Color each block nucleotide at each locations
« Reply #7 on: May 27, 2021, 06:55:32 pm »
In PyMOL, type: help dssr_block, you will see the following usage info:

Code: [Select]
dssr_block [ selection [, state [, block_file [, block_depth [, block_color [, name [, exe ]]]]]]]
From the DSSR-PyMOL paper on NAR (https://doi.org/10.1093/nar/gkaa426), download the Supplementary PDF. Section 3.2 in on "The --block-color option". In PyMOL, you use block_color, as documented from help dssr_block.

Combined, you would do the following in PyMOL:

Code: Text
  1. # manual selection, named 'sele'; color any base red
  2. dssr_block sele, block_color='N:red'

PyMOL has a flexible selection engine you may want to get familiar with.

Best regards,

Xiang-Jun

Offline spark159

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Re: Color each block nucleotide at each locations
« Reply #8 on: July 09, 2021, 03:30:09 pm »
Thank you for your kind answer!

Yes, I understood the color-option in the article but this setting will color "all" nucleotide of same kinds into a single color.
For example, color all Guanine by yellow.

But I want to do this:
color G at position 4 by yellow but Gs at position 5, 10, 11 by blue, etc

Do you have any idea to do that?

Offline spark159

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Re: Color each block nucleotide at each locations
« Reply #9 on: July 09, 2021, 03:33:40 pm »
And manual selection of a particular nucleotide in particular position didn't help as I post i the earlier thread:
It only change the color of real nucleotide in the block not the block itself....

Offline xiangjun

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Re: Color each block nucleotide at each locations
« Reply #10 on: July 09, 2021, 03:49:05 pm »
OK. Let's forget about coloring DSSR blocks for the moment, focusing exclusively on PyMOL coloring of residues.

Could you color each nucleotide at each locations in PyMOL?

Now let G4 be G at position 4, the following will color its DSSR block yellow:

Code: Bash
  1. select G4, resi 4
  2. dssr_block G4, block_color='G:yellow'
  3. # OR combined the above two steps as below:
  4. # dssr_block resi 4, block_color='N:yellow'

Let Gs be selection of Gs at postions 5, 10, 11, do the following to color their blocks blue:

Code: Bash
  1. select Gs, resi 5+10+11
  2. dssr_block Gs, block_color='G:blue'
  3. # OR combined as below:
  4. # dssr_block resi 5+10+11, block_color='N:blue'

HTH,

Xiang-Jun
« Last Edit: July 10, 2021, 10:09:41 am by xiangjun »

Offline spark159

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Re: Color each block nucleotide at each locations
« Reply #11 on: July 23, 2021, 05:54:17 pm »
Thank you so much for helpful information!

Yes, I tried and finally manage to color differently at each nucleotide blocks.
But it is quite slow since it make all individual block object for every nucleotide.

Do you have any suggest to do this more efficient way?


This is pml code I used to do this.

reinitialize
fetch 5O9G
hide all

create protein, chain A+C+B+E+D+G+F+H+W
set cartoon_color, purpleblue, protein
set cartoon_transparency, 0.6889, protein
show cartoon, protein

create na_I, chain I
set cartoon_nucleic_acid_color, red, na_I
show cartoon, na_I

create na_J, chain J
set cartoon_nucleic_acid_color, green, na_J
show cartoon, na_J

select C3_prime, name C3'
show sphere, C3_prime
set sphere_scale, 0.2, C3_prime
color gray90, C3_prime

set cartoon_ladder_mode, 1
set cartoon_ladder_radius, 0.1
set cartoon_ladder_color, black

set cartoon_tube_radius, 0.16889
set cartoon_nucleic_acid_mode, 1

dssr_block (chain I and resi 0), block_color='N:[0.0 0.3 1.0]'
dssr_block (chain I and resi 1), block_color='N:[0.0 0.786 1.0]'
dssr_block (chain I and resi 2), block_color='N:[0.123 1.0 0.844]'
dssr_block (chain I and resi 3), block_color='N:[0.781 1.0 0.187]'
dssr_block (chain I and resi 4), block_color='N:[0.642 1.0 0.326]'
dssr_block (chain I and resi 5), block_color='N:[0.0 0.0 0.536]'
dssr_block (chain I and resi 6), block_color='N:[1.0 0.887 0.0]'
dssr_block (chain I and resi 7), block_color='N:[0.313 1.0 0.655]'
dssr_block (chain I and resi 8), block_color='N:[0.0 0.692 1.0]'
dssr_block (chain I and resi 9), block_color='N:[1.0 0.175 0.0]'
dssr_block (chain I and resi 10), block_color='N:[1.0 0.393 0.0]'
dssr_block (chain I and resi 11), block_color='N:[0.047 0.959 0.92]'
dssr_block (chain I and resi 12), block_color='N:[0.0 0.724 1.0]'
dssr_block (chain I and resi 13), block_color='N:[0.212 1.0 0.756]'
dssr_block (chain I and resi 14), block_color='N:[1.0 0.727 0.0]'
dssr_block (chain I and resi 15), block_color='N:[0.0 0.0 0.678]'
dssr_block (chain I and resi 16), block_color='N:[0.66 0.0 0.0]'
dssr_block (chain I and resi 17), block_color='N:[0.0 0.316 1.0]'
dssr_block (chain I and resi 18), block_color='N:[0.0 0.0 0.536]'
dssr_block (chain I and resi 19), block_color='N:[0.0 0.0 0.732]'
dssr_block (chain I and resi 20), block_color='N:[0.0 0.0 0.785]'
dssr_block (chain I and resi 21), block_color='N:[0.0 0.206 1.0]'
dssr_block (chain I and resi 22), block_color='N:[0.0 0.535 1.0]'
dssr_block (chain I and resi 23), block_color='N:[1.0 0.291 0.0]'
dssr_block (chain I and resi 24), block_color='N:[1.0 0.349 0.0]'
dssr_block (chain I and resi 25), block_color='N:[0.839 0.0 0.0]'
dssr_block (chain I and resi 26), block_color='N:[0.0 0.755 1.0]'
dssr_block (chain I and resi 27), block_color='N:[0.693 1.0 0.275]'
dssr_block (chain I and resi 28), block_color='N:[0.0 0.363 1.0]'
dssr_block (chain I and resi 29), block_color='N:[0.0 0.331 1.0]'
dssr_block (chain I and resi 30), block_color='N:[0.821 0.0 0.0]'
dssr_block (chain I and resi 31), block_color='N:[1.0 0.625 0.0]'
dssr_block (chain I and resi 32), block_color='N:[0.0 0.457 1.0]'
dssr_block (chain I and resi 33), block_color='N:[0.262 1.0 0.705]'
dssr_block (chain I and resi 34), block_color='N:[0.0 0.598 1.0]'
dssr_block (chain I and resi 35), block_color='N:[1.0 0.669 0.0]'
dssr_block (chain I and resi 36), block_color='N:[1.0 0.088 0.0]'
dssr_block (chain I and resi 37), block_color='N:[0.0 0.786 1.0]'
dssr_block (chain I and resi 38), block_color='N:[0.553 1.0 0.414]'
dssr_block (chain I and resi 39), block_color='N:[1.0 0.669 0.0]'
dssr_block (chain I and resi 40), block_color='N:[0.0 0.0 0.536]'
dssr_block (chain I and resi 41), block_color='N:[1.0 0.582 0.0]'
dssr_block (chain I and resi 42), block_color='N:[0.338 1.0 0.629]'
dssr_block (chain I and resi 43), block_color='N:[0.0 0.065 1.0]'
dssr_block (chain I and resi 44), block_color='N:[1.0 0.48 0.0]'
dssr_block (chain I and resi 45), block_color='N:[0.0 0.849 1.0]'
dssr_block (chain I and resi 46), block_color='N:[0.541 1.0 0.427]'
dssr_block (chain I and resi 47), block_color='N:[0.0 0.849 1.0]'
dssr_block (chain I and resi 48), block_color='N:[1.0 0.901 0.0]'
dssr_block (chain I and resi 49), block_color='N:[0.0 0.033 1.0]'
dssr_block (chain I and resi 50), block_color='N:[0.0 0.018 1.0]'
dssr_block (chain I and resi 51), block_color='N:[0.0 0.065 1.0]'
dssr_block (chain I and resi 52), block_color='N:[1.0 0.872 0.0]'
dssr_block (chain I and resi 53), block_color='N:[0.756 1.0 0.212]'
dssr_block (chain I and resi 54), block_color='N:[0.0 0.0 0.999]'
dssr_block (chain I and resi 55), block_color='N:[0.731 1.0 0.237]'
dssr_block (chain I and resi 56), block_color='N:[0.0 0.049 1.0]'
dssr_block (chain I and resi 57), block_color='N:[0.0 0.676 1.0]'
dssr_block (chain I and resi 58), block_color='N:[0.0 0.0 0.625]'
dssr_block (chain I and resi 59), block_color='N:[0.963 0.044 0.0]'
dssr_block (chain I and resi 60), block_color='N:[1.0 0.335 0.0]'
dssr_block (chain I and resi 61), block_color='N:[0.073 0.99 0.895]'
dssr_block (chain I and resi 62), block_color='N:[0.92 1.0 0.047]'
dssr_block (chain I and resi 63), block_color='N:[0.351 1.0 0.617]'
dssr_block (chain I and resi 64), block_color='N:[0.225 1.0 0.743]'
dssr_block (chain I and resi 65), block_color='N:[0.528 1.0 0.44]'
dssr_block (chain I and resi 66), block_color='N:[0.022 0.927 0.946]'
dssr_block (chain I and resi 67), block_color='N:[1.0 0.814 0.0]'
dssr_block (chain I and resi 68), block_color='N:[0.0 0.52 1.0]'
dssr_block (chain I and resi 69), block_color='N:[0.0 0.865 0.996]'
dssr_block (chain I and resi 70), block_color='N:[0.625 0.0 0.0]'
dssr_block (chain I and resi 71), block_color='N:[0.174 1.0 0.794]'
dssr_block (chain I and resi 72), block_color='N:[0.882 1.0 0.085]'
dssr_block (chain I and resi 73), block_color='N:[0.0 0.0 0.821]'
dssr_block (chain I and resi 74), block_color='N:[0.0 0.488 1.0]'
dssr_block (chain I and resi 75), block_color='N:[0.553 0.0 0.0]'
dssr_block (chain I and resi 76), block_color='N:[0.0 0.0 0.767]'
dssr_block (chain I and resi 77), block_color='N:[0.0 0.018 1.0]'
dssr_block (chain I and resi 78), block_color='N:[0.705 1.0 0.262]'
dssr_block (chain I and resi 79), block_color='N:[0.0 0.0 0.981]'
dssr_block (chain I and resi 80), block_color='N:[0.427 1.0 0.541]'
dssr_block (chain I and resi 81), block_color='N:[0.0 0.0 0.553]'
dssr_block (chain I and resi 82), block_color='N:[0.803 0.0 0.0]'
dssr_block (chain I and resi 83), block_color='N:[0.262 1.0 0.705]'
dssr_block (chain I and resi 84), block_color='N:[0.0 0.441 1.0]'
dssr_block (chain I and resi 85), block_color='N:[0.136 1.0 0.832]'
dssr_block (chain I and resi 86), block_color='N:[0.0 0.363 1.0]'
dssr_block (chain I and resi 87), block_color='N:[0.0 0.504 1.0]'
dssr_block (chain I and resi 88), block_color='N:[0.009 0.912 0.958]'
dssr_block (chain I and resi 89), block_color='N:[0.0 0.629 1.0]'
dssr_block (chain I and resi -2), block_color='N:[1.0 0.16 0.0]'
dssr_block (chain I and resi -72), block_color='N:[0.402 1.0 0.566]'
dssr_block (chain I and resi -71), block_color='N:[0.0 0.582 1.0]'
dssr_block (chain I and resi -70), block_color='N:[0.696 0.0 0.0]'
dssr_block (chain I and resi -69), block_color='N:[0.0 0.0 0.981]'
dssr_block (chain I and resi -68), block_color='N:[0.0 0.41 1.0]'
dssr_block (chain I and resi -67), block_color='N:[0.693 1.0 0.275]'
dssr_block (chain I and resi -66), block_color='N:[0.0 0.018 1.0]'
dssr_block (chain I and resi -65), block_color='N:[0.022 0.927 0.946]'
dssr_block (chain I and resi -64), block_color='N:[0.047 0.959 0.92]'
dssr_block (chain I and resi -63), block_color='N:[0.806 1.0 0.161]'
dssr_block (chain I and resi -62), block_color='N:[0.718 1.0 0.25]'
dssr_block (chain I and resi -61), block_color='N:[0.0 0.0 0.803]'
dssr_block (chain I and resi -60), block_color='N:[1.0 0.204 0.0]'
dssr_block (chain I and resi -59), block_color='N:[0.819 1.0 0.149]'
dssr_block (chain I and resi -58), block_color='N:[0.553 0.0 0.0]'
dssr_block (chain I and resi -57), block_color='N:[0.465 1.0 0.503]'
dssr_block (chain I and resi -56), block_color='N:[1.0 0.771 0.0]'
dssr_block (chain I and resi -55), block_color='N:[1.0 0.422 0.0]'
dssr_block (chain I and resi -54), block_color='N:[0.0 0.504 1.0]'
dssr_block (chain I and resi -53), block_color='N:[0.0 0.0 0.696]'
dssr_block (chain I and resi -52), block_color='N:[0.971 0.959 0.0]'
dssr_block (chain I and resi -51), block_color='N:[0.642 1.0 0.326]'
dssr_block (chain I and resi -50), block_color='N:[1.0 0.248 0.0]'
dssr_block (chain I and resi -49), block_color='N:[0.0 0.833 1.0]'
dssr_block (chain I and resi -48), block_color='N:[0.536 0.0 0.0]'
dssr_block (chain I and resi -47), block_color='N:[0.0 0.0 0.981]'
dssr_block (chain I and resi -46), block_color='N:[1.0 0.901 0.0]'
dssr_block (chain I and resi -45), block_color='N:[0.44 1.0 0.528]'
dssr_block (chain I and resi -44), block_color='N:[0.0 0.175 1.0]'
dssr_block (chain I and resi -43), block_color='N:[0.0 0.645 1.0]'
dssr_block (chain I and resi -42), block_color='N:[0.642 1.0 0.326]'
dssr_block (chain I and resi -41), block_color='N:[0.571 0.0 0.0]'
dssr_block (chain I and resi -40), block_color='N:[1.0 0.814 0.0]'
dssr_block (chain I and resi -39), block_color='N:[0.0 0.708 1.0]'
dssr_block (chain I and resi -38), block_color='N:[0.225 1.0 0.743]'
dssr_block (chain I and resi -37), block_color='N:[0.0 0.567 1.0]'
dssr_block (chain I and resi -36), block_color='N:[0.87 1.0 0.098]'
dssr_block (chain I and resi -35), block_color='N:[0.971 0.959 0.0]'
dssr_block (chain I and resi -34), block_color='N:[0.199 1.0 0.769]'
dssr_block (chain I and resi -33), block_color='N:[0.136 1.0 0.832]'
dssr_block (chain I and resi -32), block_color='N:[1.0 0.712 0.0]'
dssr_block (chain I and resi -31), block_color='N:[1.0 0.436 0.0]'
dssr_block (chain I and resi -30), block_color='N:[0.767 0.0 0.0]'
dssr_block (chain I and resi -29), block_color='N:[0.0 0.0 0.946]'
dssr_block (chain I and resi -28), block_color='N:[0.262 1.0 0.705]'
dssr_block (chain I and resi -27), block_color='N:[0.553 0.0 0.0]'
dssr_block (chain I and resi -26), block_color='N:[0.92 1.0 0.047]'
dssr_block (chain I and resi -25), block_color='N:[0.478 1.0 0.49]'
dssr_block (chain I and resi -24), block_color='N:[0.0 0.0 0.732]'
dssr_block (chain I and resi -23), block_color='N:[0.009 0.912 0.958]'
dssr_block (chain I and resi -22), block_color='N:[0.478 1.0 0.49]'
dssr_block (chain I and resi -21), block_color='N:[0.882 1.0 0.085]'
dssr_block (chain I and resi -20), block_color='N:[0.0 0.112 1.0]'
dssr_block (chain I and resi -19), block_color='N:[0.3 1.0 0.667]'
dssr_block (chain I and resi -18), block_color='N:[0.0 0.441 1.0]'
dssr_block (chain I and resi -17), block_color='N:[0.0 0.127 1.0]'
dssr_block (chain I and resi -16), block_color='N:[0.981 0.059 0.0]'
dssr_block (chain I and resi -15), block_color='N:[0.06 0.975 0.908]'
dssr_block (chain I and resi -14), block_color='N:[0.0 0.645 1.0]'
dssr_block (chain I and resi -13), block_color='N:[0.0 0.425 1.0]'
dssr_block (chain I and resi -12), block_color='N:[0.0 0.237 1.0]'
dssr_block (chain I and resi -11), block_color='N:[0.136 1.0 0.832]'
dssr_block (chain I and resi -10), block_color='N:[1.0 0.8 0.0]'
dssr_block (chain I and resi -9), block_color='N:[0.364 1.0 0.604]'
dssr_block (chain I and resi -8), block_color='N:[0.0 0.033 1.0]'
dssr_block (chain I and resi -7), block_color='N:[1.0 0.8 0.0]'
dssr_block (chain I and resi -6), block_color='N:[0.895 1.0 0.073]'
dssr_block (chain I and resi -5), block_color='N:[0.0 0.0 0.518]'
dssr_block (chain I and resi -4), block_color='N:[0.667 1.0 0.3]'
dssr_block (chain I and resi -3), block_color='N:[0.91 0.001 0.0]'
dssr_block (chain I and resi -1), block_color='N:[1.0 0.32 0.0]'

dssr_block (chain J and resi 0), block_color='N:[0.0 0.159 1.0]'
dssr_block (chain J and resi 1), block_color='N:[0.427 1.0 0.541]'
dssr_block (chain J and resi 2), block_color='N:[1.0 0.422 0.0]'
dssr_block (chain J and resi 3), block_color='N:[1.0 0.291 0.0]'
dssr_block (chain J and resi 4), block_color='N:[0.0 0.645 1.0]'
dssr_block (chain J and resi 5), block_color='N:[1.0 0.175 0.0]'
dssr_block (chain J and resi 6), block_color='N:[0.629 1.0 0.338]'
dssr_block (chain J and resi 7), block_color='N:[0.794 1.0 0.174]'
dssr_block (chain J and resi 8), block_color='N:[0.0 0.676 1.0]'
dssr_block (chain J and resi 9), block_color='N:[1.0 0.858 0.0]'
dssr_block (chain J and resi 10), block_color='N:[0.0 0.535 1.0]'
dssr_block (chain J and resi 11), block_color='N:[1.0 0.277 0.0]'
dssr_block (chain J and resi 12), block_color='N:[0.0 0.52 1.0]'
dssr_block (chain J and resi 13), block_color='N:[0.174 1.0 0.794]'
dssr_block (chain J and resi 14), block_color='N:[0.376 1.0 0.591]'
dssr_block (chain J and resi 15), block_color='N:[0.0 0.0 1.0]'
dssr_block (chain J and resi 16), block_color='N:[0.0 0.0 0.518]'
dssr_block (chain J and resi 17), block_color='N:[0.892 0.0 0.0]'
dssr_block (chain J and resi 18), block_color='N:[0.174 1.0 0.794]'
dssr_block (chain J and resi 19), block_color='N:[0.0 0.159 1.0]'
dssr_block (chain J and resi 20), block_color='N:[0.0 0.0 0.536]'
dssr_block (chain J and resi 21), block_color='N:[0.0 0.394 1.0]'
dssr_block (chain J and resi 22), block_color='N:[0.073 0.99 0.895]'
dssr_block (chain J and resi 23), block_color='N:[0.571 0.0 0.0]'
dssr_block (chain J and resi 24), block_color='N:[0.908 1.0 0.06]'
dssr_block (chain J and resi 25), block_color='N:[0.958 0.974 0.009]'
dssr_block (chain J and resi 26), block_color='N:[0.963 0.044 0.0]'
dssr_block (chain J and resi 27), block_color='N:[0.821 0.0 0.0]'
dssr_block (chain J and resi 28), block_color='N:[0.136 1.0 0.832]'
dssr_block (chain J and resi 29), block_color='N:[0.0 0.488 1.0]'
dssr_block (chain J and resi 30), block_color='N:[0.0 0.159 1.0]'
dssr_block (chain J and resi 31), block_color='N:[0.693 1.0 0.275]'
dssr_block (chain J and resi 32), block_color='N:[1.0 0.451 0.0]'
dssr_block (chain J and resi 33), block_color='N:[0.0 0.629 1.0]'
dssr_block (chain J and resi 34), block_color='N:[0.999 0.073 0.0]'
dssr_block (chain J and resi 35), block_color='N:[0.0 0.896 0.971]'
dssr_block (chain J and resi 36), block_color='N:[0.832 1.0 0.136]'
dssr_block (chain J and resi 37), block_color='N:[0.0 0.0 0.5]'
dssr_block (chain J and resi 38), block_color='N:[0.625 0.0 0.0]'
dssr_block (chain J and resi 39), block_color='N:[0.0 0.0 0.5]'
dssr_block (chain J and resi 40), block_color='N:[0.0 0.818 1.0]'
dssr_block (chain J and resi 41), block_color='N:[0.553 1.0 0.414]'
dssr_block (chain J and resi 42), block_color='N:[0.0 0.253 1.0]'
dssr_block (chain J and resi 43), block_color='N:[0.0 0.0 1.0]'
dssr_block (chain J and resi 44), block_color='N:[0.503 1.0 0.465]'
dssr_block (chain J and resi 45), block_color='N:[0.0 0.316 1.0]'
dssr_block (chain J and resi 46), block_color='N:[0.035 0.943 0.933]'
dssr_block (chain J and resi 47), block_color='N:[0.389 1.0 0.579]'
dssr_block (chain J and resi 48), block_color='N:[0.731 1.0 0.237]'
dssr_block (chain J and resi 49), block_color='N:[0.874 0.0 0.0]'
dssr_block (chain J and resi 50), block_color='N:[0.528 1.0 0.44]'
dssr_block (chain J and resi 51), block_color='N:[0.0 0.0 0.981]'
dssr_block (chain J and resi 52), block_color='N:[1.0 0.291 0.0]'
dssr_block (chain J and resi 53), block_color='N:[0.503 1.0 0.465]'
dssr_block (chain J and resi 54), block_color='N:[0.655 1.0 0.313]'
dssr_block (chain J and resi 55), block_color='N:[0.0 0.0 0.767]'
dssr_block (chain J and resi 56), block_color='N:[1.0 0.393 0.0]'
dssr_block (chain J and resi 57), block_color='N:[0.389 1.0 0.579]'
dssr_block (chain J and resi 58), block_color='N:[0.667 1.0 0.3]'
dssr_block (chain J and resi 59), block_color='N:[1.0 0.175 0.0]'
dssr_block (chain J and resi 60), block_color='N:[0.769 1.0 0.199]'
dssr_block (chain J and resi 61), block_color='N:[0.288 1.0 0.68]'
dssr_block (chain J and resi 62), block_color='N:[0.731 1.0 0.237]'
dssr_block (chain J and resi 63), block_color='N:[0.0 0.0 0.732]'
dssr_block (chain J and resi 64), block_color='N:[0.68 1.0 0.288]'
dssr_block (chain J and resi 65), block_color='N:[0.161 1.0 0.806]'
dssr_block (chain J and resi 66), block_color='N:[0.0 0.896 0.971]'
dssr_block (chain J and resi 67), block_color='N:[0.3 1.0 0.667]'
dssr_block (chain J and resi 68), block_color='N:[0.693 1.0 0.275]'
dssr_block (chain J and resi 69), block_color='N:[0.0 0.833 1.0]'
dssr_block (chain J and resi 70), block_color='N:[0.0 0.441 1.0]'
dssr_block (chain J and resi 71), block_color='N:[1.0 0.248 0.0]'
dssr_block (chain J and resi 72), block_color='N:[0.629 1.0 0.338]'
dssr_block (chain J and resi -1), block_color='N:[0.91 0.001 0.0]'
dssr_block (chain J and resi -89), block_color='N:[0.882 1.0 0.085]'
dssr_block (chain J and resi -88), block_color='N:[0.0 0.08 1.0]'
dssr_block (chain J and resi -87), block_color='N:[0.111 1.0 0.857]'
dssr_block (chain J and resi -86), block_color='N:[0.0 0.739 1.0]'
dssr_block (chain J and resi -85), block_color='N:[0.617 1.0 0.351]'
dssr_block (chain J and resi -84), block_color='N:[0.0 0.0 0.571]'
dssr_block (chain J and resi -83), block_color='N:[1.0 0.538 0.0]'
dssr_block (chain J and resi -82), block_color='N:[0.0 0.0 0.714]'
dssr_block (chain J and resi -81), block_color='N:[0.0 0.582 1.0]'
dssr_block (chain J and resi -80), block_color='N:[0.0 0.567 1.0]'
dssr_block (chain J and resi -79), block_color='N:[0.0 0.0 1.0]'
dssr_block (chain J and resi -78), block_color='N:[0.0 0.865 0.996]'
dssr_block (chain J and resi -77), block_color='N:[0.91 0.001 0.0]'
dssr_block (chain J and resi -76), block_color='N:[0.806 1.0 0.161]'
dssr_block (chain J and resi -75), block_color='N:[0.414 1.0 0.553]'
dssr_block (chain J and resi -74), block_color='N:[0.0 0.0 0.839]'
dssr_block (chain J and resi -73), block_color='N:[0.0 0.0 0.696]'
dssr_block (chain J and resi -72), block_color='N:[0.0 0.316 1.0]'
dssr_block (chain J and resi -71), block_color='N:[0.0 0.0 1.0]'
dssr_block (chain J and resi -70), block_color='N:[1.0 0.306 0.0]'
dssr_block (chain J and resi -69), block_color='N:[0.0 0.0 0.553]'
dssr_block (chain J and resi -68), block_color='N:[0.0 0.52 1.0]'
dssr_block (chain J and resi -67), block_color='N:[1.0 0.916 0.0]'
dssr_block (chain J and resi -66), block_color='N:[0.0 0.378 1.0]'
dssr_block (chain J and resi -65), block_color='N:[0.839 0.0 0.0]'
dssr_block (chain J and resi -64), block_color='N:[0.5 0.0 0.0]'
dssr_block (chain J and resi -63), block_color='N:[0.161 1.0 0.806]'
dssr_block (chain J and resi -62), block_color='N:[1.0 0.901 0.0]'
dssr_block (chain J and resi -61), block_color='N:[1.0 0.436 0.0]'
dssr_block (chain J and resi -60), block_color='N:[0.0 0.143 1.0]'
dssr_block (chain J and resi -59), block_color='N:[0.0 0.0 0.821]'
dssr_block (chain J and resi -58), block_color='N:[0.0 0.786 1.0]'
dssr_block (chain J and resi -57), block_color='N:[0.0 0.284 1.0]'
dssr_block (chain J and resi -56), block_color='N:[0.009 0.912 0.958]'
dssr_block (chain J and resi -55), block_color='N:[1.0 0.8 0.0]'
dssr_block (chain J and resi -54), block_color='N:[0.0 0.0 0.589]'
dssr_block (chain J and resi -53), block_color='N:[1.0 0.611 0.0]'
dssr_block (chain J and resi -52), block_color='N:[0.625 0.0 0.0]'
dssr_block (chain J and resi -51), block_color='N:[1.0 0.146 0.0]'
dssr_block (chain J and resi -50), block_color='N:[0.767 0.0 0.0]'
dssr_block (chain J and resi -49), block_color='N:[1.0 0.131 0.0]'
dssr_block (chain J and resi -48), block_color='N:[0.0 0.0 0.999]'
dssr_block (chain J and resi -47), block_color='N:[0.212 1.0 0.756]'
dssr_block (chain J and resi -46), block_color='N:[0.0 0.0 0.857]'
dssr_block (chain J and resi -45), block_color='N:[0.503 1.0 0.465]'
dssr_block (chain J and resi -44), block_color='N:[0.0 0.0 1.0]'
dssr_block (chain J and resi -43), block_color='N:[0.0 0.0 0.625]'
dssr_block (chain J and resi -42), block_color='N:[0.123 1.0 0.844]'
dssr_block (chain J and resi -41), block_color='N:[0.678 0.0 0.0]'
dssr_block (chain J and resi -40), block_color='N:[1.0 0.814 0.0]'
dssr_block (chain J and resi -39), block_color='N:[1.0 0.538 0.0]'
dssr_block (chain J and resi -38), block_color='N:[0.0 0.096 1.0]'
dssr_block (chain J and resi -37), block_color='N:[1.0 0.277 0.0]'
dssr_block (chain J and resi -36), block_color='N:[0.149 1.0 0.819]'
dssr_block (chain J and resi -35), block_color='N:[0.0 0.786 1.0]'
dssr_block (chain J and resi -34), block_color='N:[0.731 1.0 0.237]'
dssr_block (chain J and resi -33), block_color='N:[0.0 0.708 1.0]'
dssr_block (chain J and resi -32), block_color='N:[1.0 0.683 0.0]'
dssr_block (chain J and resi -31), block_color='N:[0.819 1.0 0.149]'
dssr_block (chain J and resi -30), block_color='N:[1.0 0.843 0.0]'
dssr_block (chain J and resi -29), block_color='N:[1.0 0.8 0.0]'
dssr_block (chain J and resi -28), block_color='N:[0.66 0.0 0.0]'
dssr_block (chain J and resi -27), block_color='N:[0.3 1.0 0.667]'
dssr_block (chain J and resi -26), block_color='N:[1.0 0.901 0.0]'
dssr_block (chain J and resi -25), block_color='N:[0.0 0.425 1.0]'
dssr_block (chain J and resi -24), block_color='N:[0.0 0.0 0.839]'
dssr_block (chain J and resi -23), block_color='N:[0.0 0.504 1.0]'
dssr_block (chain J and resi -22), block_color='N:[0.769 1.0 0.199]'
dssr_block (chain J and resi -21), block_color='N:[0.0 0.0 0.518]'
dssr_block (chain J and resi -20), block_color='N:[0.0 0.629 1.0]'
dssr_block (chain J and resi -19), block_color='N:[1.0 0.204 0.0]'
dssr_block (chain J and resi -18), block_color='N:[0.0 0.441 1.0]'
dssr_block (chain J and resi -17), block_color='N:[0.035 0.943 0.933]'
dssr_block (chain J and resi -16), block_color='N:[0.874 0.0 0.0]'
dssr_block (chain J and resi -15), block_color='N:[0.0 0.802 1.0]'
dssr_block (chain J and resi -14), block_color='N:[0.928 0.015 0.0]'
dssr_block (chain J and resi -13), block_color='N:[0.3 1.0 0.667]'
dssr_block (chain J and resi -12), block_color='N:[1.0 0.756 0.0]'
dssr_block (chain J and resi -11), block_color='N:[0.0 0.0 1.0]'
dssr_block (chain J and resi -10), block_color='N:[0.92 1.0 0.047]'
dssr_block (chain J and resi -9), block_color='N:[0.0 0.08 1.0]'
dssr_block (chain J and resi -8), block_color='N:[0.009 0.912 0.958]'
dssr_block (chain J and resi -7), block_color='N:[0.882 1.0 0.085]'
dssr_block (chain J and resi -6), block_color='N:[0.262 1.0 0.705]'
dssr_block (chain J and resi -5), block_color='N:[0.0 0.0 0.643]'
dssr_block (chain J and resi -4), block_color='N:[0.0 0.378 1.0]'
dssr_block (chain J and resi -3), block_color='N:[1.0 0.814 0.0]'
dssr_block (chain J and resi -2), block_color='N:[0.642 1.0 0.326]'

bg_color white
remove solvent
hide everything, hydro

util.cbaw
set sphere_quality, 4
set stick_quality, 16

set depth_cue, 0
set ray_trace_fog, 0

set ray_shadow, off
set orthoscopic, 1

set antialias, 1
set valence, 0

set ambient, 0.68
set reflect, 0
set direct, 0.6
set spec_direct, 0
set light_count, 1

zoom complete=1
ray 1800
png 5O9G_test_block.png




« Last Edit: July 23, 2021, 05:58:42 pm by spark159 »

Offline spark159

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Re: Color each block nucleotide at each locations
« Reply #12 on: July 23, 2021, 05:56:15 pm »
And also it print lots of warning messages during the run.
I can't locate the origin of this warning.



Time used: 00:00:00:00
PyMOL>dssr_block (chain J and resi 56), block_color='N:[1.0 0.393 0.0]'

Processing file '/tmp/tmpinhy880j.pdb'
   more than one < P  > atoms in J.DG56
   *****the first match is used*****
   more than one < OP1> atoms in J.DG56
   *****the first match is used*****
   more than one < OP2> atoms in J.DG56
   *****the first match is used*****
   more than one < O5'> atoms in J.DG56
   *****the first match is used*****
   more than one < C5'> atoms in J.DG56
   *****the first match is used*****
   more than one < C4'> atoms in J.DG56
   *****the first match is used*****
   more than one < O4'> atoms in J.DG56
   *****the first match is used*****
   more than one < C3'> atoms in J.DG56
   *****the first match is used*****
   more than one < O3'> atoms in J.DG56
   *****the first match is used*****
   more than one < C2'> atoms in J.DG56
   *****the first match is used*****
   more than one < C1'> atoms in J.DG56
   *****the first match is used*****
   more than one < N9 > atoms in J.DG56
   *****the first match is used*****
   more than one < C4 > atoms in J.DG56
   *****the first match is used*****
   more than one < C8 > atoms in J.DG56
   *****the first match is used*****

Offline xiangjun

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Re: Color each block nucleotide at each locations
« Reply #13 on: July 23, 2021, 06:17:33 pm »
Quote
Yes, I tried and finally manage to color differently at each nucleotide blocks.

Glad to know that you have managed to color nucleotide blocks as desired. This is an important first step for later on speed optimizations.

Quote
But it is quite slow since it make all individual block object for every nucleotide.


How many colors do you want to have? Grouping nucleotides with the same color should speed up the process. It is now a matter of PyMOL selection syntax to play with.

Quote
And also it print lots of warning messages during the run.
I can't locate the origin of this warning.
PyMOL>dssr_block (chain J and resi 56), block_color='N:[1.0 0.393 0.0]'

I cannot reproduce the warning messages. Let's not worry about them right now.

Best regards,

Xiang-Jun


 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.